Variant report

Variant	rs11608250
Chromosome Location	chr12:104196501-104196502
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr12:104195876-104196607	A549	lung:	n/a	n/a
2	FOSL2	chr12:104195640-104196698	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:104196029-104196557	SK-N-SH	brain:	n/a	n/a
4	JUND	chr12:104195702-104196765	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr12:104196056-104196584	SK-N-SH_RA	brain:	n/a	n/a
6	TEAD4	chr12:104195785-104196671	SK-N-SH	brain:	n/a	n/a
7	EP300	chr12:104195923-104196612	A549	lung:	n/a	n/a
8	NR3C1	chr12:104196041-104196547	A549	lung:	n/a	n/a
9	RXRA	chr12:104195911-104196776	SK-N-SH	brain:	n/a	chr12:104196601-104196610
10	JUND	chr12:104195766-104196701	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr12:104195758-104196673	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr12:104195829-104196638	A549	lung:	n/a	n/a
13	TCF12	chr12:104195446-104196953	SK-N-SH	brain:	n/a	chr12:104195531-104195541
14	TAF1	chr12:104196324-104196572	SK-N-SH	brain:	n/a	n/a
15	SIN3AK20	chr12:104195954-104196535	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr12:104196488-104196544	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr12:104195870-104196754	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr12:104195652-104196878	SK-N-SH	brain:	n/a	n/a
19	EP300	chr12:104195984-104196549	SK-N-SH_RA	brain:	n/a	n/a
20	RXRA	chr12:104195935-104196617	SK-N-SH	brain:	n/a	chr12:104196601-104196610
21	EP300	chr12:104195965-104196595	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr12:104195482-104196842	SK-N-SH	brain:	n/a	n/a
23	PBX3	chr12:104195747-104196756	SK-N-SH	brain:	n/a	n/a
24	MAX	chr12:104195856-104196650	SK-N-SH	brain:	n/a	n/a
25	MAX	chr12:104195878-104196660	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr12:104195797-104196885	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr12:104195607-104196723	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr12:104195952-104196675	SK-N-SH	brain:	n/a	n/a
29	NFIC	chr12:104195854-104196723	SK-N-SH	brain:	n/a	n/a
30	NFIC	chr12:104195651-104196701	SK-N-SH	brain:	n/a	n/a
31	SP1	chr12:104195876-104196582	A549	lung:	n/a	n/a
32	GATA3	chr12:104195626-104196966	SK-N-SH	brain:	n/a	n/a
33	ZBTB33	chr12:104195929-104196645	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
2	chr12:104183990..104193430-chr12:104193641..104204611,16	MCF-7	breast:
3	chr12:104196315..104200600-chr12:104233023..104235965,5	MCF-7	breast:
4	chr12:104190724..104195360-chr12:104196501..104199658,6	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1043469	0.82[LWK][hapmap];0.82[MKK][hapmap]
rs11610831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11611059	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11615701	0.83[EUR][1000 genomes]
rs11616182	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11835188	0.81[YRI][hapmap]
rs2292688	0.90[LWK][hapmap]
rs59330576	0.81[AMR][1000 genomes]
rs59991655	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61939571	0.81[AMR][1000 genomes]
rs7139029	0.85[CEU][hapmap]
rs73175815	0.82[EUR][1000 genomes]
rs73192037	0.82[AFR][1000 genomes]
rs73192039	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11608250	DRAM1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:104185800-104198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:104187400-104206800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:104187800-104198200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:104187800-104212600	Weak transcription	GM12878-XiMat	blood
11	chr12:104190800-104198800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:104190800-104201800	Weak transcription	Gastric	stomach
13	chr12:104190800-104204400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:104191000-104209800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:104191000-104211800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:104192000-104200400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:104192600-104206600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:104192800-104197000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:104192800-104199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:104193000-104196600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:104193000-104196800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:104193400-104196600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:104193400-104197000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:104193400-104197000	Enhancers	Fetal Muscle Leg	muscle
26	chr12:104193600-104196800	Enhancers	HepG2	liver
27	chr12:104193600-104196800	Enhancers	HSMM	muscle
28	chr12:104193600-104204000	Weak transcription	Primary T cells from cord blood	blood
29	chr12:104193800-104198200	Genic enhancers	K562	blood
30	chr12:104194000-104206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:104194400-104196600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:104194400-104197000	Enhancers	NH-A	brain
33	chr12:104194400-104207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:104194600-104196600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:104194600-104196600	Enhancers	Brain Angular Gyrus	brain
36	chr12:104194600-104196600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:104194600-104196800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:104194600-104196800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr12:104194600-104197000	Enhancers	Psoas Muscle	Psoas
40	chr12:104194600-104197200	Enhancers	Osteobl	bone
41	chr12:104194600-104197600	Enhancers	Rectal Smooth Muscle	rectum
42	chr12:104194600-104198800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:104194600-104199400	Weak transcription	Esophagus	oesophagus
44	chr12:104194600-104199600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:104194600-104199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:104194600-104203800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:104194600-104207000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:104194600-104214600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:104194600-104214800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:104194800-104196600	Enhancers	Skeletal Muscle Male	skeletal muscle

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