Variant report

Variant	rs7572631
Chromosome Location	chr2:10760574-10760575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10759541..10761460-chr2:10768691..10771124,2	K562	blood:
2	chr2:10732866..10735426-chr2:10759991..10761967,2	MCF-7	breast:
3	chr2:10754918..10757554-chr2:10759036..10761540,2	K562	blood:

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10167129	0.86[YRI][hapmap]
rs10178247	0.90[ASN][1000 genomes]
rs10181806	0.86[YRI][hapmap]
rs10191883	0.86[YRI][hapmap]
rs10195255	0.90[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs10195802	0.86[YRI][hapmap]
rs10201077	0.86[YRI][hapmap]
rs10203664	0.86[YRI][hapmap]
rs10203785	0.90[YRI][hapmap]
rs10210859	0.86[YRI][hapmap]
rs10454738	0.86[YRI][hapmap]
rs10929686	0.86[YRI][hapmap]
rs10929688	0.86[YRI][hapmap]
rs11683335	0.86[YRI][hapmap]
rs12464908	0.90[YRI][hapmap]
rs12692415	0.86[YRI][hapmap]
rs12692416	0.86[YRI][hapmap]
rs12692417	0.90[YRI][hapmap]
rs12692418	0.86[YRI][hapmap]
rs12995159	0.86[YRI][hapmap]
rs12995602	0.85[YRI][hapmap]
rs13005359	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13034061	0.86[YRI][hapmap]
rs1309	0.86[LWK][hapmap]
rs1586623	0.81[ASN][1000 genomes]
rs17364568	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1990612	0.86[YRI][hapmap]
rs2010080	0.86[YRI][hapmap]
rs2110775	0.81[ASN][1000 genomes]
rs2110776	0.86[YRI][hapmap]
rs2110778	0.86[YRI][hapmap]
rs2287061	0.85[LWK][hapmap]
rs2287062	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs2357654	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2357656	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs2884233	0.86[YRI][hapmap]
rs3814388	0.86[YRI][hapmap]
rs3815521	0.86[YRI][hapmap]
rs4233882	0.86[YRI][hapmap]
rs4233883	0.86[YRI][hapmap]
rs4331474	0.86[YRI][hapmap]
rs4453662	0.86[YRI][hapmap]
rs4470306	0.86[YRI][hapmap]
rs4519489	0.86[YRI][hapmap]
rs4555318	0.86[YRI][hapmap]
rs4613248	0.86[YRI][hapmap]
rs4614910	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs4668691	0.86[YRI][hapmap]
rs4669593	0.86[YRI][hapmap]
rs4669598	0.88[YRI][hapmap]
rs4669599	0.86[YRI][hapmap]
rs4669605	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4669606	0.83[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap]
rs55674834	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6432109	0.86[YRI][hapmap]
rs6432110	0.86[YRI][hapmap]
rs6432111	0.86[YRI][hapmap]
rs6432112	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs6432113	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs6432114	0.86[YRI][hapmap]
rs6432115	0.82[YRI][hapmap]
rs6432116	0.86[YRI][hapmap]
rs6432117	0.86[YRI][hapmap]
rs6432119	0.89[YRI][hapmap]
rs6432120	0.86[YRI][hapmap]
rs6432122	0.86[YRI][hapmap]
rs6432126	0.82[YRI][hapmap]
rs6706542	0.86[YRI][hapmap]
rs6709466	0.86[YRI][hapmap]
rs6710033	0.82[YRI][hapmap]
rs6712406	0.86[YRI][hapmap]
rs6714413	0.86[YRI][hapmap]
rs6715461	0.82[ASN][1000 genomes]
rs6719701	0.90[YRI][hapmap]
rs6721510	0.86[YRI][hapmap]
rs6721514	0.86[YRI][hapmap]
rs6721739	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs6725354	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727884	0.86[YRI][hapmap]
rs6733416	0.86[YRI][hapmap]
rs6735074	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs6744599	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs6744854	0.86[YRI][hapmap]
rs6750891	0.86[YRI][hapmap]
rs6751075	0.86[YRI][hapmap]
rs6751398	0.86[YRI][hapmap]
rs6755548	0.86[YRI][hapmap]
rs6759714	0.86[YRI][hapmap]
rs6761678	0.86[YRI][hapmap]
rs715246	0.86[YRI][hapmap]
rs715247	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs72777328	0.80[ASN][1000 genomes]
rs72777332	0.81[ASN][1000 genomes]
rs728135	0.86[YRI][hapmap]
rs728281	0.86[YRI][hapmap]
rs728282	0.83[LWK][hapmap];0.86[YRI][hapmap]
rs728283	0.89[YRI][hapmap]
rs7355649	0.86[YRI][hapmap]
rs7563816	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs7563894	0.86[YRI][hapmap]
rs7566767	0.86[YRI][hapmap]
rs7566875	0.86[YRI][hapmap]
rs7582775	0.86[YRI][hapmap]
rs7587114	0.86[YRI][hapmap]
rs7587231	0.86[YRI][hapmap]
rs7592691	0.86[YRI][hapmap]
rs7593496	0.86[YRI][hapmap]
rs759398	0.94[CHB][hapmap];0.84[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs759403	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs7600495	0.86[YRI][hapmap]
rs7600587	0.86[YRI][hapmap]
rs7600695	0.86[YRI][hapmap]
rs7600728	0.86[YRI][hapmap]
rs7600820	0.86[YRI][hapmap]
rs7601748	0.86[YRI][hapmap]
rs7605461	0.86[YRI][hapmap]
rs7608498	0.86[YRI][hapmap]
rs9287720	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv833370	chr2:10625149-10785402	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7572631	PDIA6	cis	parietal	SCAN
rs7572631	CYS1	cis	cerebellum	SCAN
rs7572631	C2orf50	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10725600-10793400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:10725800-10787000	Weak transcription	Fetal Heart	heart
3	chr2:10729400-10781800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:10729400-10798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:10730800-10774400	Weak transcription	Psoas Muscle	Psoas
6	chr2:10732000-10777600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:10738400-10766600	Weak transcription	Fetal Kidney	kidney
8	chr2:10740200-10782000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:10742400-10773800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:10742400-10774400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:10742600-10760800	Weak transcription	Ovary	ovary
12	chr2:10742600-10772200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:10742600-10791000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:10742800-10760600	Weak transcription	Brain Anterior Caudate	brain
15	chr2:10742800-10782400	Weak transcription	Esophagus	oesophagus
16	chr2:10743800-10760800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:10744400-10777000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:10745200-10772400	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:10746000-10760600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:10746400-10764000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:10746600-10760600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:10746600-10760800	Weak transcription	Fetal Thymus	thymus
23	chr2:10746600-10761000	Weak transcription	Aorta	Aorta
24	chr2:10746600-10761000	Weak transcription	Left Ventricle	heart
25	chr2:10746600-10777000	Weak transcription	Colonic Mucosa	Colon
26	chr2:10746600-10781800	Weak transcription	Right Ventricle	heart
27	chr2:10746800-10760600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:10746800-10761000	Weak transcription	Gastric	stomach
29	chr2:10746800-10774000	Weak transcription	Spleen	Spleen
30	chr2:10746800-10774400	Weak transcription	HSMMtube	muscle
31	chr2:10746800-10781800	Weak transcription	Pancreas	Pancrea
32	chr2:10747000-10781800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:10749400-10774200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:10753600-10792800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:10754600-10760800	Weak transcription	Fetal Intestine Small	intestine
36	chr2:10754800-10796000	Weak transcription	Small Intestine	intestine
37	chr2:10755200-10760600	Weak transcription	Fetal Intestine Large	intestine
38	chr2:10755600-10772400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:10755800-10760600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:10755800-10761000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:10756000-10760600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:10756000-10767200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:10756000-10772200	Weak transcription	HMEC	breast
44	chr2:10756200-10795800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:10756200-10828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:10756800-10762200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:10756800-10763000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:10757000-10764400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:10757000-10765800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:10757000-10765800	Strong transcription	Monocytes-CD14+_RO01746	blood

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