Variant report

Variant	rs1796041
Chromosome Location	chr2:97627260-97627261
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97480973..97483903-chr2:97621623..97628750,6	MCF-7	breast:
2	chr2:97534921..97536780-chr2:97625343..97628032,2	K562	blood:
3	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
4	chr2:97620122..97624045-chr2:97625118..97628656,4	MCF-7	breast:
5	chr2:97536159..97540837-chr2:97622900..97627821,5	K562	blood:
6	chr2:97557941..97560811-chr2:97624763..97627667,2	MCF-7	breast:
7	chr2:97610586..97615218-chr2:97625029..97628319,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000252845	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10202644	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1257000	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1257008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1257009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1257011	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1257012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1257015	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1257016	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1257017	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1257018	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1257019	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1257020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1257027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1257028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1257029	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1257114	0.81[ASN][1000 genomes]
rs1268682	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12717787	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016654	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13021723	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1623881	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1624844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1730106	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1730111	0.86[AMR][1000 genomes]
rs1730119	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1730120	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1730122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1730123	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1730124	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1730126	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1730128	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1730129	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1730130	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1730131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1796027	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796028	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796032	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796038	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796044	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796045	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1796047	0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1796049	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707304	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs34434950	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4263148	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4366944	0.92[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4586672	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6576992	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6576993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6576994	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6576995	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6576997	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6576999	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707255	0.86[AMR][1000 genomes]
rs6714860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6715329	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6725927	0.82[CHB][hapmap]
rs6757916	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7569434	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7584318	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584335	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7593493	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7597743	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1796041		cis	Lymphoblastoid	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97619600-97628400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:97620400-97629400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:97620600-97628200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:97620800-97627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:97620800-97629600	Weak transcription	Fetal Intestine Small	intestine
6	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
7	chr2:97623400-97628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:97624200-97629800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:97625400-97629600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:97625600-97627400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:97625600-97627400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:97625600-97627600	Enhancers	Colonic Mucosa	Colon
13	chr2:97625600-97628200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:97625600-97628400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:97625600-97630600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:97625600-97631200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:97625600-97634200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:97625800-97627400	Enhancers	Primary T cells from cord blood	blood
19	chr2:97625800-97627600	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:97625800-97628400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:97626000-97627400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:97626000-97627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:97626000-97627600	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:97626000-97628400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:97626000-97628400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:97626000-97629000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:97626000-97629800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:97626000-97631000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:97626200-97629200	Weak transcription	Spleen	Spleen
30	chr2:97626200-97630400	Enhancers	Dnd41	blood
31	chr2:97626200-97635800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:97626400-97628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:97626400-97629600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:97626400-97629600	Enhancers	GM12878-XiMat	blood
35	chr2:97626400-97630200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:97626600-97628600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:97626600-97629200	Enhancers	Primary B cells from peripheral blood	blood
38	chr2:97626600-97629800	Enhancers	Fetal Thymus	thymus
39	chr2:97626600-97631800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:97626600-97631800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:97626800-97627400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:97626800-97628400	Weak transcription	HMEC	breast
43	chr2:97626800-97628400	Weak transcription	NHEK	skin
44	chr2:97626800-97628800	Weak transcription	Placenta	Placenta
45	chr2:97626800-97629200	Enhancers	Primary hematopoietic stem cells	blood
46	chr2:97626800-97629200	Weak transcription	Esophagus	oesophagus
47	chr2:97626800-97629400	Enhancers	Primary B cells from cord blood	blood
48	chr2:97626800-97633000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:97627000-97627600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:97627000-97627800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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