Variant report

Variant	rs1004626
Chromosome Location	chr1:217201404-217201405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:217200941..217201873-chr6:54053550..54054293,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10863289	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11117756	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11807917	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1416530	0.88[ASN][1000 genomes]
rs1416531	0.88[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs17636912	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789551	0.82[GIH][hapmap]
rs4085455	0.88[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4846804	0.85[EUR][1000 genomes]
rs61816725	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61816726	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688120	0.92[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs6694626	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7538474	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217194800-217206200	Weak transcription	Left Ventricle	heart
2	chr1:217196000-217206200	Weak transcription	Right Atrium	heart
3	chr1:217196200-217206200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:217198600-217203200	Weak transcription	Aorta	Aorta
5	chr1:217199200-217204800	Enhancers	Fetal Kidney	kidney
6	chr1:217199600-217202400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:217199600-217203800	Enhancers	Fetal Intestine Large	intestine
8	chr1:217199600-217206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:217199600-217211800	Weak transcription	Gastric	stomach
10	chr1:217199800-217202800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:217199800-217203400	Enhancers	Fetal Intestine Small	intestine
12	chr1:217200000-217201800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:217200000-217202000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:217200000-217203600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:217200200-217203200	Weak transcription	Pancreas	Pancrea
16	chr1:217200400-217202400	Weak transcription	Stomach Mucosa	stomach
17	chr1:217200400-217202600	Weak transcription	Psoas Muscle	Psoas
18	chr1:217200400-217203000	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:217200600-217201800	Enhancers	Brain Anterior Caudate	brain
20	chr1:217200600-217204000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:217200800-217201800	Enhancers	Brain Substantia Nigra	brain
22	chr1:217200800-217202200	Weak transcription	Small Intestine	intestine
23	chr1:217201000-217201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:217201000-217206000	Weak transcription	Fetal Heart	heart
25	chr1:217201200-217202200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:217201200-217202400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:217201400-217202400	Weak transcription	Duodenum Mucosa	Duodenum

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