Variant report

Variant	rs620643
Chromosome Location	chr8:103112417-103112418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103054616..103056405-chr8:103111193..103113703,2	MCF-7	breast:
2	chr8:103111624..103115089-chr8:103119935..103122230,3	MCF-7	breast:
3	chr8:103084257..103086284-chr8:103112303..103114668,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1269692	0.91[CHB][hapmap]
rs1269727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496936	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498666	0.91[CHB][hapmap]
rs503374	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs503985	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs509608	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs523474	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs533390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533489	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs533695	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs556388	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs561070	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs582862	0.87[ASN][1000 genomes]
rs591500	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs604234	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs610125	0.95[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs622553	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs635670	0.87[CHB][hapmap]
rs637403	0.91[CHB][hapmap]
rs652008	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659398	0.85[ASN][1000 genomes]
rs688431	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891232	chr8:103001914-103138045	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv891233	chr8:103001914-103162638	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv891234	chr8:103020391-103113701	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv891235	chr8:103032394-103162638	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv891237	chr8:103039917-103113701	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv891238	chr8:103055520-103116959	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv891239	chr8:103056517-103162638	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
8	nsv891240	chr8:103070301-103162638	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
9	esv2754264	chr8:103070824-103170824	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv891241	chr8:103079505-103162638	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
12	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs620643	GRHL2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103104600-103112600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:103104800-103118800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr8:103106000-103117600	Weak transcription	Fetal Heart	heart
4	chr8:103107600-103114400	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:103108400-103118800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr8:103108400-103120000	Weak transcription	Gastric	stomach
7	chr8:103108600-103114600	Weak transcription	Psoas Muscle	Psoas
8	chr8:103108800-103112800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:103109000-103112600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:103109800-103120000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:103110200-103117600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr8:103110400-103112800	Weak transcription	Ovary	ovary
13	chr8:103110400-103113600	Weak transcription	Fetal Brain Female	brain
14	chr8:103110400-103114600	Weak transcription	Lung	lung
15	chr8:103110600-103114600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:103110600-103114600	Weak transcription	Left Ventricle	heart
17	chr8:103110600-103116400	Weak transcription	Primary T cells from cord blood	blood
18	chr8:103110600-103116800	Weak transcription	GM12878-XiMat	blood
19	chr8:103110800-103115600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr8:103111000-103115000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:103111200-103112600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:103111200-103113200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr8:103111400-103116200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:103111400-103116800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr8:103111600-103116200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr8:103112200-103113200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr8:103112200-103113400	Enhancers	Fetal Kidney	kidney
28	chr8:103112200-103113600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:103112200-103114800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr8:103112400-103112800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr8:103112400-103112800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr8:103112400-103113000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr8:103112400-103113200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr8:103112400-103115000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr8:103112400-103115400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:103112400-103117800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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