Variant report

Variant	rs7602807
Chromosome Location	chr2:96012907-96012908
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95831424..95833102-chr2:96012448..96013993,2	MCF-7	breast:
2	chr2:96012877..96014896-chr2:96015583..96018073,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163067	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10195614	0.92[EUR][1000 genomes]
rs10874471	0.84[AMR][1000 genomes]
rs1104775	0.88[EUR][1000 genomes]
rs11164122	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11897976	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468777	0.82[AMR][1000 genomes]
rs12992066	0.86[EUR][1000 genomes]
rs1559483	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862897	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966272	0.81[EUR][1000 genomes]
rs2042477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098768	0.81[EUR][1000 genomes]
rs2113417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2113419	0.82[AMR][1000 genomes]
rs2278065	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2320339	0.89[EUR][1000 genomes]
rs3755518	0.98[AFR][1000 genomes]
rs3755519	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755521	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755523	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755525	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772031	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772032	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772033	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772034	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3772037	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772041	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772042	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772043	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3772044	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821341	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4283455	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854249	0.83[EUR][1000 genomes]
rs4854251	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58610630	0.84[AMR][1000 genomes]
rs6577012	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6577013	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715813	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750542	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7574862	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7580685	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585914	0.87[EUR][1000 genomes]
rs7586229	0.87[EUR][1000 genomes]
rs7594144	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869185	0.93[AFR][1000 genomes]
rs870393	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889851	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889852	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889853	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9678800	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989786	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv482871	chr2:95936531-96036880	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv2757818	chr2:95970138-96152559	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	esv2759076	chr2:95970138-96152559	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv998543	chr2:95979772-96074212	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv535825	chr2:95979772-96074212	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv582496	chr2:95999856-96020029	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv829578	chr2:96010192-96015186	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv3321815	chr2:96010750-96013598	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3437070	chr2:96011450-96013998	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	esv3504135	chr2:96011525-96013598	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	esv3504136	chr2:96011525-96013598	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	nsv829579	chr2:96011563-96014374	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7602807	KCNIP3	cis	Thyroid	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96011000-96013000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:96011000-96013000	Active TSS	Aorta	Aorta
3	chr2:96011000-96013200	Active TSS	HSMM	muscle
4	chr2:96011200-96013000	Bivalent/Poised TSS	Thymus	Thymus
5	chr2:96011200-96013000	Active TSS	NHLF	lung
6	chr2:96011200-96013200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr2:96011200-96013200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:96011200-96013200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:96011200-96013400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:96011400-96013000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:96011400-96013000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:96011400-96013000	Active TSS	Brain Angular Gyrus	brain
13	chr2:96011400-96013000	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:96011400-96013000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:96011400-96013000	Active TSS	Placenta Amnion	Placenta Amnion
16	chr2:96011400-96013200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:96011400-96013200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr2:96011400-96013200	Active TSS	Left Ventricle	heart
19	chr2:96011400-96013200	Active TSS	Right Atrium	heart
20	chr2:96011800-96013000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:96011800-96013200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:96011800-96013200	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr2:96012000-96013000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:96012000-96013000	Active TSS	NH-A	brain
25	chr2:96012000-96013200	Enhancers	Liver	Liver
26	chr2:96012200-96013000	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:96012400-96013000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:96012600-96013000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr2:96012600-96013000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:96012600-96013000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:96012600-96013000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:96012600-96013000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:96012600-96013000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
34	chr2:96012600-96013000	Flanking Active TSS	Lung	lung
35	chr2:96012600-96013000	Flanking Active TSS	Psoas Muscle	Psoas
36	chr2:96012600-96013000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:96012600-96013000	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr2:96012600-96013200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr2:96012600-96013200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:96012600-96013200	Flanking Active TSS	Right Ventricle	heart
41	chr2:96012600-96013200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr2:96012600-96013400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr2:96012600-96013400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr2:96012600-96014000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:96012600-96014200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:96012800-96013000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:96012800-96013000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:96012800-96013000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:96012800-96013000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:96012800-96013000	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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