Variant report

Variant	rs10930561
Chromosome Location	chr2:173421249-173421250
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	POLR2A	chr2:173420038-173421535	GM12878	blood:	n/a	n/a
2	MAZ	chr2:173420152-173421433	Hela-S3	cervix:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663
3	HEY1	chr2:173420044-173421582	K562	blood:	n/a	chr2:173420723-173420738 chr2:173420648-173420663
4	POLR2A	chr2:173419900-173421978	IMR90	lung:	n/a	n/a
5	MAX	chr2:173421024-173421731	K562	blood:	n/a	chr2:173421339-173421354 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
6	MAZ	chr2:173420011-173421758	IMR90	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
7	POLR2A	chr2:173419978-173421476	SK-N-MC	brain:	n/a	n/a
8	TCF7L2	chr2:173420176-173421435	HCT-116	colon:	n/a	n/a
9	TCF3	chr2:173421201-173421431	GM12878	blood:	n/a	chr2:173421348-173421364
10	PAX5	chr2:173420162-173421485	GM12892	blood:	n/a	chr2:173420605-173420614
11	CTBP2	chr2:173420223-173421477	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:173420109-173422237	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:173420089-173421467	Hela-S3	cervix:	n/a	n/a
14	CHD2	chr2:173421100-173421607	K562	blood:	n/a	n/a
15	GABPA	chr2:173420356-173421498	K562	blood:	n/a	chr2:173420383-173420390
16	TBP	chr2:173420040-173421702	K562	blood:	n/a	n/a
17	MAX	chr2:173420050-173421939	Hela-S3	cervix:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
18	CBX3	chr2:173420983-173421739	K562	blood:	n/a	n/a
19	POLR2A	chr2:173419917-173421649	GM18951	blood:	n/a	n/a
20	MXI1	chr2:173419823-173421871	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:173420041-173421556	HUVEC	blood vessel:	n/a	n/a
22	MAX	chr2:173419949-173421893	A549	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
23	POLR2A	chr2:173421057-173421342	SK-N-SH	brain:	n/a	n/a
24	MXI1	chr2:173420312-173421789	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr2:173420075-173421861	A549	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
26	TAF1	chr2:173420008-173421519	HepG2	liver:	n/a	n/a
27	USF1	chr2:173421145-173421789	K562	blood:	n/a	n/a
28	POLR2A	chr2:173420264-173421508	GM12891	blood:	n/a	n/a
29	MYC	chr2:173420205-173421472	MCF-7	breast:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663
30	HDAC2	chr2:173421013-173421584	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIN3AK20	chr2:173421008-173421670	MCF-7	breast:	n/a	n/a
32	POLR2A	chr2:173420001-173421520	H1-neurons	neurons:	n/a	n/a
33	TCF3	chr2:173420293-173421564	GM12878	blood:	n/a	chr2:173421348-173421364
34	ETS1	chr2:173420616-173421495	GM12878	blood:	n/a	chr2:173420755-173420766 chr2:173421037-173421052 chr2:173420729-173420740
35	CREB1	chr2:173420046-173421519	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:173420181-173421309	K562	blood:	n/a	n/a
37	POU2F2	chr2:173421245-173421608	GM12878	blood:	n/a	chr2:173421461-173421479 chr2:173421466-173421474 chr2:173421465-173421474
38	MAX	chr2:173420091-173421807	NB4	blood:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
39	POLR2A	chr2:173421089-173421550	GM12878	blood:	n/a	n/a
40	TCF7L2	chr2:173421037-173421502	Hela-S3	cervix:	n/a	n/a
41	HCFC1	chr2:173420066-173421658	K562	blood:	n/a	n/a
42	POLR2A	chr2:173420144-173421433	Gliobla	brain:	n/a	n/a
43	POLR2A	chr2:173420076-173421546	GM18505	blood:	n/a	n/a
44	POLR2A	chr2:173420061-173421694	HepG2	liver:	n/a	n/a
45	MAX	chr2:173419988-173421946	ECC-1	luminal epithelium:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
46	NRF1	chr2:173420019-173422138	SK-N-SH	brain:	n/a	chr2:173420724-173420735 chr2:173420383-173420390
47	EP300	chr2:173421163-173421309	K562	blood:	n/a	n/a
48	KAP1	chr2:173420144-173421473	U2OS	brain:	n/a	n/a
49	YY1	chr2:173421039-173421376	GM12892	blood:	n/a	n/a
50	USF1	chr2:173421198-173421809	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:173420452..173421308-chr5:90678657..90679530,2	Hela-S3	cervix:
2	chr2:172966170..172969056-chr2:173419829..173422762,2	MCF-7	breast:
3	chr2:173421239..173421739-chr7:141437473..141437989,2	Hela-S3	cervix:
4	chr2:173420097..173422198-chr2:173422510..173426199,4	K562	blood:
5	chr2:173418979..173421868-chr2:173434562..173438051,3	K562	blood:
6	chr2:173351396..173353492-chr2:173418976..173421854,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-4	chr2:173420817-173421324	ENSG00000225205.1
2	lnc-DLX2-4	chr2:173420817-173421257	ENSG00000225205.1

Variant related genes	Relation type
PDK1	TF binding region
ENSG00000225205	TF binding region
ENSG00000199866	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000152256	Chromatin interaction
ENSG00000091409	Chromatin interaction
ENSG00000228775	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1010752	0.88[ASN][1000 genomes]
rs10181851	0.93[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1075638	0.80[ASN][1000 genomes]
rs10930559	0.82[CHB][hapmap]
rs10930562	0.93[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10930563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930564	1.00[EUR][1000 genomes]
rs10930565	0.81[ASN][1000 genomes]
rs10930566	0.86[ASN][1000 genomes]
rs10930567	0.86[ASN][1000 genomes]
rs10930568	0.80[ASN][1000 genomes]
rs11904158	0.93[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs12465512	0.86[ASN][1000 genomes]
rs12467086	1.00[EUR][1000 genomes]
rs12613307	0.86[CHB][hapmap]
rs12617037	0.80[ASN][1000 genomes]
rs12620518	0.80[ASN][1000 genomes]
rs12622724	0.83[CHB][hapmap]
rs13019331	0.81[ASN][1000 genomes]
rs1530864	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1530865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1531148	0.84[ASN][1000 genomes]
rs1531149	0.84[ASN][1000 genomes]
rs16860438	0.85[CHB][hapmap]
rs16860478	0.82[CHB][hapmap]
rs16860513	0.85[CHB][hapmap]
rs16860515	0.82[CHB][hapmap]
rs16860634	0.82[CHB][hapmap]
rs16860693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293645	0.82[CHB][hapmap]
rs2293648	0.82[CHB][hapmap]
rs34051646	0.81[ASN][1000 genomes]
rs3765065	0.93[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769321	0.93[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs60127617	0.80[ASN][1000 genomes]
rs61505737	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62167835	0.83[ASN][1000 genomes]
rs6710129	0.93[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6718681	0.86[ASN][1000 genomes]
rs6719140	0.86[ASN][1000 genomes]
rs6738196	0.93[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6752386	0.87[ASN][1000 genomes]
rs70937083	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs70937084	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7584769	0.81[ASN][1000 genomes]
rs8179584	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836628	0.86[ASN][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv3035	chr2:173419058-173463901	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173419000-173423400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:173419200-173421400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:173419200-173422400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:173419400-173421600	Active TSS	Brain Cingulate Gyrus	brain
5	chr2:173419600-173421400	Active TSS	Brain Anterior Caudate	brain
6	chr2:173419600-173421400	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr2:173419600-173421400	Active TSS	Rectal Smooth Muscle	rectum
8	chr2:173419600-173421600	Active TSS	Fetal Kidney	kidney
9	chr2:173419600-173421600	Active TSS	Pancreas	Pancrea
10	chr2:173419600-173422000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr2:173419800-173421400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr2:173419800-173421400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:173419800-173421400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:173419800-173421400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:173419800-173421400	Active TSS	Brain Substantia Nigra	brain
16	chr2:173419800-173421600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:173419800-173421600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:173419800-173421600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:173419800-173421600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:173419800-173421600	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:173419800-173421600	Active TSS	A549	lung
22	chr2:173419800-173421800	Active TSS	Right Ventricle	heart
23	chr2:173419800-173422000	Active TSS	Right Atrium	heart
24	chr2:173419800-173422600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:173419800-173423400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:173420000-173421400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:173420000-173421400	Active TSS	Aorta	Aorta
28	chr2:173420000-173421400	Active TSS	Colon Smooth Muscle	Colon
29	chr2:173420000-173421400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr2:173420000-173421400	Active TSS	Fetal Brain Female	brain
31	chr2:173420000-173421600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:173420000-173421600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr2:173420000-173421600	Active TSS	Esophagus	oesophagus
34	chr2:173420000-173421600	Active TSS	Lung	lung
35	chr2:173420000-173421600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:173420000-173421600	Active TSS	NHDF-Ad	bronchial
37	chr2:173420000-173421800	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:173420000-173421800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:173420000-173421800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:173420000-173421800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:173420000-173421800	Active TSS	Left Ventricle	heart
42	chr2:173420000-173421800	Active TSS	Ovary	ovary
43	chr2:173420000-173421800	Active TSS	Psoas Muscle	Psoas
44	chr2:173420000-173422000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:173420000-173422000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:173420000-173422000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:173420000-173422800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:173420000-173422800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr2:173420000-173423000	Active TSS	GM12878-XiMat	blood
50	chr2:173420200-173421400	Active TSS	HUES48 Cell Line	embryonic stem cell

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