Variant report

Variant	rs6711200
Chromosome Location	chr2:36923077-36923078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:36922798-36923445	MCF-7	breast:	n/a	chr2:36923101-36923115
2	CTCF	chr2:36923000-36923150	NHDF-neo	bronchial:	n/a	chr2:36923102-36923115
3	CTCF	chr2:36922940-36923090	HVMF	connective:	n/a	n/a
4	CTCF	chr2:36923045-36923164	HepG2	liver:	n/a	chr2:36923102-36923115
5	RAD21	chr2:36922950-36923296	HepG2	liver:	n/a	chr2:36923101-36923115
6	CTCF	chr2:36923040-36923190	NHLF	lung:	n/a	chr2:36923102-36923115
7	CTCF	chr2:36923060-36923210	HMEC	breast:	n/a	chr2:36923102-36923115
8	CTCF	chr2:36923041-36923168	HUVEC	blood vessel:	n/a	chr2:36923102-36923115
9	CTCF	chr2:36922960-36923110	WI-38	lung:	n/a	n/a
10	CTCF	chr2:36923010-36923172	MCF-7	breast:	n/a	chr2:36923102-36923115
11	CTCF	chr2:36923020-36923170	Hela-S3	cervix:	n/a	chr2:36923102-36923115
12	CTCF	chr2:36922748-36923427	SK-N-SH	brain:	n/a	chr2:36923102-36923115
13	CTCF	chr2:36923060-36923210	HFF	foreskin:	n/a	chr2:36923102-36923115
14	CTCF	chr2:36922992-36923201	Fibrobl	skin:	n/a	chr2:36923102-36923115
15	CTCF	chr2:36923026-36923186	MCF-7	breast:	n/a	chr2:36923102-36923115
16	RAD21	chr2:36922677-36923448	SK-N-SH	brain:	n/a	chr2:36923101-36923115
17	CTCF	chr2:36923020-36923170	AG04449	skin:	n/a	chr2:36923102-36923115
18	CTCF	chr2:36922940-36923090	HFF-Myc	foreskin:	n/a	n/a
19	CTCF	chr2:36923000-36923150	MCF-7	breast:	n/a	chr2:36923102-36923115
20	CTCF	chr2:36923019-36923166	LNCaP	prostate:	n/a	chr2:36923102-36923115
21	CTCF	chr2:36923060-36923210	HPAF	blood vessel:	n/a	chr2:36923102-36923115
22	CTCF	chr2:36923040-36923190	HA-sp	spinal cord:	n/a	chr2:36923102-36923115
23	RAD21	chr2:36922975-36923230	H1-hESC	embryonic stem cell:	n/a	chr2:36923101-36923115
24	RAD21	chr2:36922950-36923428	IMR90	lung:	n/a	chr2:36923101-36923115
25	CTCF	chr2:36922973-36923224	Gliobla	brain:	n/a	chr2:36923102-36923115
26	CTCF	chr2:36923040-36923190	NHDF-neo	bronchial:	n/a	chr2:36923102-36923115
27	CTCF	chr2:36922978-36923225	NHEK	skin:	n/a	chr2:36923102-36923115
28	CTCF	chr2:36923040-36923190	BJ	skin:	n/a	chr2:36923102-36923115
29	CTCF	chr2:36923000-36923150	RPTEC	kidney:	n/a	chr2:36923102-36923115
30	CTCF	chr2:36923045-36923175	K562	blood:	n/a	chr2:36923102-36923115
31	CTCF	chr2:36923000-36923150	K562	blood:	n/a	chr2:36923102-36923115
32	CTCF	chr2:36922980-36923207	HepG2	liver:	n/a	chr2:36923102-36923115
33	CTCF	chr2:36922973-36923223	MCF-7	breast:	n/a	chr2:36923102-36923115
34	RAD21	chr2:36922975-36923209	SK-N-SH_RA	brain:	n/a	chr2:36923101-36923115
35	CTCF	chr2:36923040-36923190	HEK293	kidney:	n/a	chr2:36923102-36923115
36	CTCF	chr2:36923020-36923170	NHEK	skin:	n/a	chr2:36923102-36923115
37	CTCF	chr2:36923040-36923190	HMF	breast:	n/a	chr2:36923102-36923115
38	CTCF	chr2:36923020-36923178	A549	lung:	n/a	chr2:36923102-36923115
39	RAD21	chr2:36922931-36923287	H1-hESC	embryonic stem cell:	n/a	chr2:36923101-36923115
40	CTCF	chr2:36923040-36923190	HPAF	blood vessel:	n/a	chr2:36923102-36923115
41	CTCF	chr2:36923020-36923170	AG09309	skin:	n/a	chr2:36923102-36923115
42	CTCF	chr2:36922960-36923110	HRPEpiC	eye:	n/a	n/a
43	CTCF	chr2:36923020-36923170	HCM	heart:	n/a	chr2:36923102-36923115
44	MAX	chr2:36922914-36923303	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr2:36923040-36923190	AG04450	lung:	n/a	chr2:36923102-36923115
46	CTCF	chr2:36922966-36923200	ProgFib	skin:	n/a	chr2:36923102-36923115
47	CTCF	chr2:36923000-36923150	BE2_C	brain:	n/a	chr2:36923102-36923115
48	RAD21	chr2:36922924-36923435	Hela-S3	cervix:	n/a	chr2:36923101-36923115
49	CTCF	chr2:36923020-36923170	HA-sp	spinal cord:	n/a	chr2:36923102-36923115
50	TCF12	chr2:36922865-36923711	SK-N-SH	brain:	n/a	chr2:36923551-36923560

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36922543..36923508-chr2:37012076..37013001,3	MCF-7	breast:
2	chr2:36922695..36923609-chr2:36997471..36998399,4	MCF-7	breast:

Variant related genes	Relation type
VIT	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10490666	0.85[JPT][hapmap]
rs11884419	0.84[EUR][1000 genomes]
rs11890551	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899717	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467423	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12989838	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638531	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346362	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722423	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6722903	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71437561	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563754	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599711	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604443	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1007757	chr2:36838387-37011384	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535643	chr2:36838387-37011384	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv873878	chr2:36908661-36942266	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv962062	chr2:36920237-36925000	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6711200	SOS1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36922400-36925200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:36922600-36923400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:36922600-36924600	Enhancers	Hela-S3	cervix
4	chr2:36922600-36924600	Enhancers	HSMM	muscle
5	chr2:36922800-36923200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:36922800-36923200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:36922800-36923200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:36922800-36923200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr2:36922800-36923200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:36922800-36923200	Enhancers	HSMMtube	muscle
11	chr2:36922800-36923200	Flanking Active TSS	NHDF-Ad	bronchial
12	chr2:36922800-36923400	Enhancers	Ovary	ovary
13	chr2:36922800-36923400	Enhancers	HUVEC	blood vessel
14	chr2:36922800-36923800	Enhancers	Adipose Nuclei	Adipose
15	chr2:36922800-36925000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:36922800-36925200	Enhancers	Fetal Lung	lung
17	chr2:36922800-36925200	Enhancers	NH-A	brain
18	chr2:36922800-36925400	Flanking Active TSS	Osteobl	bone
19	chr2:36922800-36925800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:36922800-36925800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:36923000-36923200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:36923000-36923200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:36923000-36923200	Flanking Active TSS	NHLF	lung
24	chr2:36923000-36923400	Enhancers	HMEC	breast
25	chr2:36923000-36924000	Flanking Active TSS	NHEK	skin

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