Variant report

Variant	rs7594004
Chromosome Location	chr2:39454834-39454835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39348043..39352382-chr2:39450241..39456710,6	K562	blood:
2	chr2:39287527..39289050-chr2:39453888..39455986,2	K562	blood:
3	chr2:39346597..39349702-chr2:39453282..39455044,3	MCF-7	breast:
4	chr2:39407371..39407923-chr2:39454464..39455003,2	MCF-7	breast:
5	chr2:39346582..39349686-chr2:39454756..39458494,4	MCF-7	breast:
6	chr2:39346079..39347931-chr2:39453857..39455685,2	K562	blood:
7	chr2:39286188..39287216-chr2:39454531..39455924,7	MCF-7	breast:
8	chr2:39346611..39348848-chr2:39454530..39456606,2	K562	blood:
9	chr2:38976938..38979508-chr2:39454441..39457000,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10174268	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10178527	0.89[ASN][1000 genomes]
rs10199708	0.95[AFR][1000 genomes]
rs10865146	0.91[EUR][1000 genomes]
rs10865147	0.91[ASN][1000 genomes]
rs11124661	0.84[EUR][1000 genomes]
rs11124663	0.97[EUR][1000 genomes]
rs11673802	0.92[EUR][1000 genomes]
rs11677985	0.92[EUR][1000 genomes]
rs11689688	0.92[EUR][1000 genomes]
rs12165133	0.84[EUR][1000 genomes]
rs13005378	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13028683	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1510113	0.82[AFR][1000 genomes]
rs1548170	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1976594	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2136638	0.84[EUR][1000 genomes]
rs2373527	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708222	0.85[ASN][1000 genomes]
rs2708223	0.85[ASN][1000 genomes]
rs4670917	0.83[EUR][1000 genomes]
rs6544209	0.91[EUR][1000 genomes]
rs6544210	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6544211	0.98[EUR][1000 genomes]
rs6706711	0.86[AFR][1000 genomes]
rs6712921	0.80[ASN][1000 genomes]
rs6753194	0.84[EUR][1000 genomes]
rs6759501	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761679	0.92[EUR][1000 genomes]
rs7562981	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7563373	0.84[EUR][1000 genomes]
rs7563858	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569441	0.82[EUR][1000 genomes]
rs7569834	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7573535	0.94[EUR][1000 genomes]
rs7581973	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7583149	0.84[ASN][1000 genomes]
rs7583170	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7584676	0.92[EUR][1000 genomes]
rs7590889	0.85[EUR][1000 genomes]
rs7596120	0.88[EUR][1000 genomes]
rs7607761	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv1000658	chr2:39374206-39466374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
18	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7594004	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39419000-39455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:39423400-39470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:39429800-39459600	Weak transcription	HSMM	muscle
4	chr2:39431600-39455000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:39431800-39455200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:39435400-39455600	Weak transcription	Left Ventricle	heart
7	chr2:39439400-39455200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:39442600-39455000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:39443800-39455000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:39447200-39455000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:39447600-39455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:39447600-39456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:39449200-39477600	Weak transcription	HSMMtube	muscle
14	chr2:39450800-39455200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:39451400-39455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:39453200-39455200	Weak transcription	GM12878-XiMat	blood
17	chr2:39453800-39455000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr2:39453800-39455200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:39453800-39455200	Enhancers	K562	blood
20	chr2:39453800-39455400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr2:39453800-39455400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:39453800-39455600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:39454000-39455200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:39454200-39455400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:39454600-39455000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr2:39454600-39455400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:39454600-39455600	Enhancers	H9 Cell Line	embryonic stem cell
28	chr2:39454600-39456000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr2:39454600-39456200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr2:39454800-39455000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:39454800-39455000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:39454800-39455000	Enhancers	Brain Anterior Caudate	brain
33	chr2:39454800-39455000	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:39454800-39455000	Enhancers	Colon Smooth Muscle	Colon
35	chr2:39454800-39455000	Flanking Active TSS	HepG2	liver
36	chr2:39454800-39455200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:39454800-39455200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:39454800-39455200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr2:39454800-39455200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:39454800-39455400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr2:39454800-39455400	Enhancers	Hela-S3	cervix
42	chr2:39454800-39455600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:39454800-39455600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:39454800-39456000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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