Variant report

Variant	rs6706041
Chromosome Location	chr2:127844407-127844408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127837291..127839948-chr2:127841422..127844629,3	K562	blood:
2	chr2:127843180..127845570-chr2:127848864..127852714,3	MCF-7	breast:
3	chr2:127841990..127844933-chr2:127856467..127858298,2	K562	blood:
4	chr2:127842780..127845072-chr2:127863578..127865079,2	K562	blood:

Variant related genes	Relation type
ENSG00000136717	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11675682	0.84[EUR][1000 genomes]
rs11679418	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11693218	0.85[EUR][1000 genomes]
rs11695424	0.91[YRI][hapmap]
rs12617750	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13019394	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2164871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856378	0.85[EUR][1000 genomes]
rs4662705	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6708935	0.96[CEU][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6709337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs730471	0.93[EUR][1000 genomes]
rs734115	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754107	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs755639	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7560621	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1002673	chr2:127801964-127860830	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1010577	chr2:127801964-127862257	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1011224	chr2:127802375-127860830	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv1003887	chr2:127802375-127862257	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1009309	chr2:127802730-127862257	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1014290	chr2:127805366-127860830	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1010084	chr2:127805366-127862257	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv997855	chr2:127806424-127857946	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
22	nsv1001673	chr2:127810478-127858634	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv1002124	chr2:127810478-127860830	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv1005423	chr2:127814781-127857751	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv997847	chr2:127814781-127858634	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv1014118	chr2:127814781-127860830	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv999224	chr2:127821207-127860830	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
28	nsv583035	chr2:127825968-127844735	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1001064	chr2:127828941-127862257	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
31	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
32	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
33	nsv1005149	chr2:127841930-127880106	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
35	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6706041	BIN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127815200-127850800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:127834400-127849000	Bivalent Enhancer	Placenta	Placenta
3	chr2:127834600-127848400	Enhancers	Brain Angular Gyrus	brain
4	chr2:127835000-127844800	Genic enhancers	Fetal Intestine Small	intestine
5	chr2:127835200-127846000	Enhancers	Fetal Intestine Large	intestine
6	chr2:127835400-127853200	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:127836600-127846000	Enhancers	Lung	lung
8	chr2:127839000-127845600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:127839400-127844600	Enhancers	Primary B cells from cord blood	blood
10	chr2:127839400-127852800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:127839600-127846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:127839600-127847800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:127839800-127844600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:127840000-127844800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:127840000-127844800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:127840000-127845600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:127840000-127848200	Enhancers	Spleen	Spleen
18	chr2:127840000-127849400	Enhancers	Fetal Thymus	thymus
19	chr2:127840200-127846000	Enhancers	NHDF-Ad	bronchial
20	chr2:127840200-127846600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:127840400-127845200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:127840800-127845400	Enhancers	Thymus	Thymus
23	chr2:127841200-127846000	Enhancers	Fetal Heart	heart
24	chr2:127841400-127845600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:127841600-127844600	Enhancers	Fetal Muscle Trunk	muscle
26	chr2:127841600-127845000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:127841800-127844800	Enhancers	Colonic Mucosa	Colon
28	chr2:127841800-127845000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:127841800-127845200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:127841800-127845600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:127842200-127844600	Enhancers	Small Intestine	intestine
32	chr2:127842200-127844800	Enhancers	Brain Anterior Caudate	brain
33	chr2:127842200-127857000	Enhancers	Psoas Muscle	Psoas
34	chr2:127842400-127844800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:127842400-127844800	Enhancers	NHLF	lung
36	chr2:127842400-127845000	Weak transcription	Fetal Brain Male	brain
37	chr2:127842400-127845200	Enhancers	Primary T cells from cord blood	blood
38	chr2:127842400-127849400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:127842400-127851200	Enhancers	Brain Substantia Nigra	brain
40	chr2:127843200-127844600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:127843200-127844800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:127843200-127845200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:127843200-127845400	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:127843200-127852000	Weak transcription	Liver	Liver
45	chr2:127843400-127844600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:127843400-127845000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:127843400-127845200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:127843600-127844600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:127843600-127844600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:127843600-127844600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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