Variant report

Variant	rs9685410
Chromosome Location	chr4:174152232-174152233
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:174098266..174101208-chr4:174151162..174153147,2	K562	blood:
2	chr4:174088948..174090599-chr4:174151207..174153338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109586	Chromatin interaction
ENSG00000245213	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10005325	0.92[EUR][1000 genomes]
rs10009959	1.00[ASN][1000 genomes]
rs10520255	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs10520256	0.92[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs11942280	0.85[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs13102038	0.81[EUR][1000 genomes]
rs13116270	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs13120215	0.85[EUR][1000 genomes]
rs13123359	0.83[EUR][1000 genomes]
rs13123399	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs13124470	0.91[CEU][hapmap]
rs13141844	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13142524	0.81[EUR][1000 genomes]
rs13150320	0.83[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs13151627	0.85[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs17059205	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17059207	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17059217	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs17059234	0.92[EUR][1000 genomes]
rs17059235	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs1991726	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2332656	0.87[ASN][1000 genomes]
rs2332657	0.84[EUR][1000 genomes]
rs2332658	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs28361970	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34718403	0.85[EUR][1000 genomes]
rs35644315	0.87[EUR][1000 genomes]
rs35679682	0.84[EUR][1000 genomes]
rs35730812	0.80[EUR][1000 genomes]
rs35796775	0.99[EUR][1000 genomes]
rs4380500	0.94[EUR][1000 genomes]
rs4608791	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639046	0.85[JPT][hapmap]
rs4695827	0.86[EUR][1000 genomes]
rs4696053	0.91[ASN][1000 genomes]
rs4696054	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs62342296	0.92[EUR][1000 genomes]
rs62342297	0.92[EUR][1000 genomes]
rs6553684	1.00[ASN][1000 genomes]
rs6553686	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822924	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6858043	0.86[EUR][1000 genomes]
rs722826	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs722827	0.85[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7661977	0.85[EUR][1000 genomes]
rs7667345	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7668473	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7670064	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7673747	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7681286	0.86[EUR][1000 genomes]
rs7694420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9684166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9991863	0.84[EUR][1000 genomes]
rs9993327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9995556	0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3468078	chr4:174149437-174156708	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3468079	chr4:174149437-174156708	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9685410	SCRG1	cis	parietal	SCAN
rs9685410	GALNT7	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174114200-174157800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:174114600-174155000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:174123600-174174200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:174126000-174156400	Weak transcription	Brain Anterior Caudate	brain
6	chr4:174126600-174155200	Weak transcription	GM12878-XiMat	blood
7	chr4:174126600-174163400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:174127000-174163600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:174127000-174163600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:174128200-174169200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:174131800-174156400	Weak transcription	Fetal Intestine Small	intestine
12	chr4:174131800-174168600	Weak transcription	Gastric	stomach
13	chr4:174136600-174158400	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:174136800-174157200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:174139000-174157600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:174140400-174158200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:174140400-174163400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr4:174140400-174163600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:174140400-174163600	Weak transcription	Aorta	Aorta
20	chr4:174140600-174158000	Weak transcription	Hela-S3	cervix
21	chr4:174140600-174158200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:174140600-174158600	Weak transcription	HSMMtube	muscle
23	chr4:174142200-174173400	Weak transcription	Lung	lung
24	chr4:174143600-174155000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:174144200-174169000	Weak transcription	Fetal Intestine Large	intestine
26	chr4:174145200-174155000	Weak transcription	Primary B cells from cord blood	blood
27	chr4:174145800-174163800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:174145800-174163800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:174148000-174152400	Weak transcription	Thymus	Thymus
30	chr4:174148000-174153200	Weak transcription	Fetal Thymus	thymus
31	chr4:174148000-174154800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:174148000-174155200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:174148000-174155400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:174148000-174156400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:174148000-174157200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:174148000-174157400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:174148000-174173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:174148200-174154000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:174148400-174154000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:174148600-174153600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:174148600-174157200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:174149200-174157000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:174149800-174152800	Enhancers	Dnd41	blood
44	chr4:174150000-174153600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr4:174150200-174163800	Weak transcription	Psoas Muscle	Psoas
46	chr4:174150200-174173400	Weak transcription	Small Intestine	intestine
47	chr4:174150400-174157800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:174150600-174153600	Enhancers	K562	blood
49	chr4:174150800-174153800	Enhancers	Primary hematopoietic stem cells	blood
50	chr4:174151200-174154000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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