Variant report

Variant	rs9995556
Chromosome Location	chr4:174136952-174136953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174099303..174100811-chr4:174136883..174138440,2	K562	blood:
2	chr4:174134665..174137165-chr4:174138818..174141532,2	K562	blood:
3	chr4:174107501..174109531-chr4:174134790..174137729,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10005325	0.93[EUR][1000 genomes]
rs10024603	0.87[AMR][1000 genomes]
rs10520255	0.92[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs10520256	1.00[CEU][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs11942280	0.92[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs13102038	0.94[EUR][1000 genomes]
rs13116270	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13117810	0.90[EUR][1000 genomes]
rs13120215	0.90[EUR][1000 genomes]
rs13123359	0.85[EUR][1000 genomes]
rs13123399	0.92[CEU][hapmap]
rs13124470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13141844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13142524	0.94[EUR][1000 genomes]
rs13150320	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs13151627	0.92[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs17059205	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17059207	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17059217	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17059235	0.92[CEU][hapmap]
rs1991726	0.92[CEU][hapmap]
rs2332657	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332658	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28361970	0.93[EUR][1000 genomes]
rs28413646	0.91[EUR][1000 genomes]
rs28694391	0.86[EUR][1000 genomes]
rs34285915	0.83[EUR][1000 genomes]
rs34718403	0.90[EUR][1000 genomes]
rs35576170	0.82[EUR][1000 genomes]
rs35644315	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35679682	0.85[EUR][1000 genomes]
rs35730812	0.85[EUR][1000 genomes]
rs35796775	0.85[EUR][1000 genomes]
rs36050097	0.82[EUR][1000 genomes]
rs4380500	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4608791	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4695827	0.91[EUR][1000 genomes]
rs4696050	0.90[EUR][1000 genomes]
rs4696054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6553686	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6822924	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6858043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722826	0.92[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs722827	0.92[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7661977	0.90[EUR][1000 genomes]
rs7667345	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7668473	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7673747	0.93[EUR][1000 genomes]
rs7689781	0.81[CEU][hapmap]
rs9685410	0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs9991863	0.96[AMR][1000 genomes];0.98[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	nsv518900	chr4:174130503-174142874	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv527434	chr4:174134684-174136952	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9995556	GALNT7	cis	cerebellum	SCAN
rs9995556	SCRG1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174112800-174140000	Weak transcription	Aorta	Aorta
3	chr4:174113800-174138000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:174114200-174157800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:174114600-174155000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:174123600-174174200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:174125600-174144800	Weak transcription	Primary B cells from cord blood	blood
8	chr4:174125800-174139200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr4:174126000-174156400	Weak transcription	Brain Anterior Caudate	brain
10	chr4:174126400-174149800	Weak transcription	Esophagus	oesophagus
11	chr4:174126600-174155200	Weak transcription	GM12878-XiMat	blood
12	chr4:174126600-174163400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr4:174126800-174139000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:174127000-174139600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:174127000-174148600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr4:174127000-174163600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:174127000-174163600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:174127400-174138200	Weak transcription	Dnd41	blood
19	chr4:174127400-174149000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:174127600-174138200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:174128200-174138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:174128200-174139000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:174128200-174169200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:174129000-174138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:174130200-174139400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:174130800-174138200	Weak transcription	Stomach Mucosa	stomach
27	chr4:174130800-174138800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:174131000-174138600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:174131000-174138800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:174131000-174139000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:174131200-174147800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:174131800-174140200	Weak transcription	Thymus	Thymus
33	chr4:174131800-174156400	Weak transcription	Fetal Intestine Small	intestine
34	chr4:174131800-174168600	Weak transcription	Gastric	stomach
35	chr4:174132400-174138400	Enhancers	K562	blood
36	chr4:174132800-174150600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:174133000-174138800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:174133000-174139000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:174133400-174138600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:174133400-174138800	Weak transcription	HSMMtube	muscle
41	chr4:174133400-174138800	Weak transcription	NHLF	lung
42	chr4:174133600-174138400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:174133600-174138400	Weak transcription	HUVEC	blood vessel
44	chr4:174133600-174138800	Weak transcription	NHDF-Ad	bronchial
45	chr4:174133800-174138200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:174134000-174138400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:174134200-174138400	Weak transcription	Hela-S3	cervix
48	chr4:174134600-174138400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:174134800-174138400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:174135800-174138800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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